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1) David was able to convince another engineer to help them.

I would be shocked if they attempted fate twice! They  were well armed the first time and only Shaw escaped.

2) They flew a much smaller ship.

I think they would want the bigger more dangerous ship...full of deadly cargo..just in case they needed it at the Engineer home world.

3) The film actually shows a Deacon Alien piloting the ship.

I think the Deacon was still toddling around the escape shuttle looking for a baby bottle...It could have tracked Shaw and David..But they were in space suits and hard to smell/track.

4) The ship was automatically activated.

I suppose Shaw flew it...Maybe you don't have to sit in the Jockey chair..until you want to fire it? play the flute push some buttons...set the course jump in Stasis chamber?

Like to see a scene with them escaping LV223 and the Deacon interfering with their plans!

'Like to see a scene with them escaping LV223 and the Deacon interfering with their plans!'

Yes, please! :)

Have thought about this too (the OP) - and to be honest don't really have any good ideas as to how they piloted the ship.

Could be that David can somehow regain control of his body and, as MZ alludes to, fly it remotely?  Perhaps Shaw sits in the pilot seat (this could serve as a cryo as well?) and pilots after a crash course from David?  This could be the start of a Giger change in Shaw?

Sadly, I don't think we will see this in AC.  Hope i'm wrong but I think seeing the ship fly off at end of Prom is as much as we will get! 

Not sure a jockey or Deacon would pilot it either, although that would be very cool!

Would have been cool to have the Deacon coming to life while Shaw is rescuing and packing up David!

Someone should cut a scene like this :

Shaw finds headless David..

*cut*

Deacon cutting itself free...

*cut*

Shaw putting David's head in bag...

*cut*

Deacon crawling from the Engineers body..

*cut*

Shaw lowering David to the ground..

*cut*

Deacon finds it's footing...

*cut*

David telling Shaw they need some foodstuff and spare Oxygen tanks from the Escape module.......

Shaw agrees, heads back.......

Movie ends.

@MonsterZero

That would make a pretty cool scene, you'd be a great editor!

5) Shaw held the wheel while David worked the pedals.

@S.M 

Haha, good one!

1) i think we can safely assume they manage to get off LV-223 with just David.

2) I would assume its exactly the same kind of Ship as the Juggernaught and it has a Cargo (we dont know if the DNA is the same though, but we can assume).

3) As far as another ship, i doubt it... as far as the one that David and Shaw left in i doubt it.. i would assume they was already to set off before the Deacon made its appearance... could be safe to assume a 12-24 hour Period for the Deacon to gestate inside the Engineer.

4) I think this is possible... i think David would need to activate a few things and set the course to Paradise and after that who knows... we dont know the workings of the Juggernaught/Derelict yet and so it would most likely have a  Auto Pilot however like with Planes on Earth its safe to assume that Manual Piloting is required for Take off and Landing and so we have to assume someone has had to be in the Pilot Chair.

I would assume David.

I always thought of David08's Dismembered head being synced up to the onboard computer of the Juggernaut & that's how they depart and continue to fly the ship while Shaw helps with Navigation ^_^

Fox or Ridley could clarify if you have to be in the Jockey chair to pilot the vehicle? (Not that they care! Lol)

Is the Jockey chair: a weapon? A telescope?

The chair in which David plays the flute, seems to be the navigation seat? It brought up the Orrery. I assume you push some buttons, play the flute, select what planet to visit, push some buttons and the ship takes you there?

If you want to Engineer the planet you're visiting?: You sit in the Space Jockey chair and fire away.

Just visiting the planet?: Enter a hypersleep chamber.

I'm with Monster 0. I suspect the central chair is some form of warp drive/ telescope/ astrometrix (thanks 7/9) set up. We have seen that controls seem to be based on the other seat and we saw that David was easily able to work out basic controls after activation using the small flute. My money is on David and Shaw flying the ship together. Where food, water etc will come from to keep Shaw alive and how David's head will be re-attached is another story. Re the Deacon. I will never forgive Ridley if it grows to become some kind of technology using humanoid rather than another even more Alien Xenomorph. I doubt it will though.

I have thought about this also. My suggestion is that Shaw put David’s head back on because in the end of the movie David says something like “I can navigate the ship”. A Deacon can’t be the pilot because it grew out of the Engineer and the Engineer was at another ship as far as I know and I doubt that there were two. One can question if a Deacon has the intelligence to learn how to fly it. The logical answer would probably be that David was the pilot to Paradise.

Hopefully there are no urns or eggs at the ship because that would be a huge risk (remember the eggs in Alien, 1979).

Ridley had confirmed that the Ship has a Cargo.... as he said David was bringing Hell with him, and then asked what if the Black Goo infected a God, or Machine.

So to me this suggests the other ship is carrying a Cargo i would maybe even go as far as to say the ship could be connected to the same Temple...

I cant remember which concept work i saw but i think i remember one that could indicate 4 Bays that means 4 Juggernauts per Temple?

I never knew that...sounds like a smart idea to take a ship carrying death to Paradise, just in case. Also lets the "Gods" know that their children don't take kindly to extermination threats, and it isn't cool to send an address to a weapons facility as an invitation(even though on some level I think that it was a test, that the majority of the Prometheus crew failed.)

Thinking out loud. Perhaps Shaw and David's ship contains more Engineers, all carrying Xeno embryo's and all still in cryo.

This post seems irrelevant now...lol...